COMPARTMENTS: unification and visualization of protein subcellular localization evidence

TY - JOUR

T1 - COMPARTMENTS

T2 - unification and visualization of protein subcellular localization evidence

AU - Binder, Janos X

AU - Pletscher-Frankild, Sune

AU - Tsafou, Kalliopi

AU - Stolte, Christian

AU - O'Donoghue, Seán I

AU - Schneider, Reinhard

AU - Jensen, Lars Juhl

PY - 2014

Y1 - 2014

N2 - Information on protein subcellular localization is important to understand the cellular functions of proteins. Currently, such information is manually curated from the literature, obtained from high-throughput microscopy-based screens and predicted from primary sequence. To get a comprehensive view of the localization of a protein, it is thus necessary to consult multiple databases and prediction tools. To address this, we present the COMPARTMENTS resource, which integrates all sources listed above as well as the results of automatic text mining. The resource is automatically kept up to date with source databases, and all localization evidence is mapped onto common protein identifiers and Gene Ontology terms. We further assign confidence scores to the localization evidence to facilitate comparison of different types and sources of evidence. To further improve the comparability, we assign confidence scores based on the type and source of the localization evidence. Finally, we visualize the unified localization evidence for a protein on a schematic cell to provide a simple overview.

AB - Information on protein subcellular localization is important to understand the cellular functions of proteins. Currently, such information is manually curated from the literature, obtained from high-throughput microscopy-based screens and predicted from primary sequence. To get a comprehensive view of the localization of a protein, it is thus necessary to consult multiple databases and prediction tools. To address this, we present the COMPARTMENTS resource, which integrates all sources listed above as well as the results of automatic text mining. The resource is automatically kept up to date with source databases, and all localization evidence is mapped onto common protein identifiers and Gene Ontology terms. We further assign confidence scores to the localization evidence to facilitate comparison of different types and sources of evidence. To further improve the comparability, we assign confidence scores based on the type and source of the localization evidence. Finally, we visualize the unified localization evidence for a protein on a schematic cell to provide a simple overview.

U2 - 10.1093/database/bau012

DO - 10.1093/database/bau012

M3 - Journal article

C2 - 24573882

SN - 1758-0463

VL - 2014

JO - Database : the journal of biological databases and curation

JF - Database : the journal of biological databases and curation

M1 - bau012

ER -